NonAlignments.py

# =============================================================================
# bmle
# G4Pipeline: NonAlignments.py
# Generates a 'non-alignment' file from a SAM file
# =============================================================================

def main(alignPath):
	"""Generate a GFF3 file of non-aligned regions from a SAM alignment file.
	
	:param alignPath: path to the SAM-formatted blastn alignment file
	:return: writes a GFF3 file of non-alignments to the same directory as alignPath
	"""
	import re
	from operator import itemgetter
	print('\nGenerating non-alignments...')
	
	# Loads alignments from SAM file
	print('Loading data...')
	entries = []
	seqs = {}
	with open(alignPath, 'r') as alignFile:
		for line in alignFile:
			temp = line.split('\t')
			if not line.startswith('@'):
				entries.append(temp)
			elif line.startswith('@SQ'):
				seqs[temp[1][3:]] = temp[2][3:]
	
	# Extracts coordinates of aligned sequences
	print('Extracting coordinates...')
	data = {k: [] for k in seqs}
	for line in entries:
		start = int(line[3])
		end = start + sum(map(int, re.findall('(\d+)(?=[MDNX=])', line[5]))) - 1
		data[line[2]].append((start, end))
	for k,v in data.items(): sorted(v, key=itemgetter(0))

	# Merges coordinates of overlapping aligned sequences
	print('Merging coordinates...')
	for k,v in data.items():
		i = 1
		while i < len(v):
			a = tuple([int(x) for x in v[i-1]])
			b = tuple([int(x) for x in v[i]])
			if not a[0] > b[1] and not a[1] < b[0]:
				data[k].remove(a)
				data[k].remove(b)
				data[k].insert(i-1, (min(a[0],b[0]), max(a[1],b[1])))
			else: i += 1
			
		# Adds filler annotations to beginning and end of sequence
		seqLen = str(int(seqs[k])+1)
		data[k].insert(0, (0, 0))
		data[k].append((seqLen, seqLen))
		
	# Inverts coordinates
	print('Inverting coordinates...')
	nalign = []
	for k,v in data.items():
		for i in range(1, len(v)):
			a = v[i-1]
			b = v[i]
			nalign.append((k, int(a[1])+1, int(b[0])-1))
	
	# Writes to GFF file
	print('Writing to file...')
	outputPath = alignPath[:-3] + 'gff3'
	with open(outputPath, 'w') as outFile:
		outFile.write('##gff-version 3\n')
		for k,v in seqs.items(): outFile.write('##sequence-region ' + k + ' 1 ' + v)
		for i, item in enumerate(nalign):
			outFile.write(item[0] + '\tblastn\tnon-alignment\t' + str(item[1]) + '\t' + str(item[2]) + '\t.\t.\t.\tID=nal_' + str(i) + ';Name=nal_' + str(i) + ';Start=' + str(item[1]) + ';End=' + str(item[2]) + '\n')
	
	print('Finished writing to ' + outputPath + '\nFinished!\n')
	
# =============================================================================

if __name__ == '__main__':
	import argparse
	
	parser = argparse.ArgumentParser(
		description='Generates a GFF file of non-aligned regions from a SAM alignment file.')
	parser.add_argument('alignPath',
						help='path to the SAM-formatted blastn alignment file')
	args = parser.parse_args()
	
	main(args.alignPath)